Kleinendorst joined the New Jersey Devils organization in 2000–01 as an assistant coach under Larry Robinson.[1] He was a scout for five years prior to assuming the head coaching position at organization's Lowell Devils AHL affiliate from 2006–07 to 2008–09.[1] On July 13, 2009, it was announced that former Devils star John MacLean would replace Kleinendorst as the head coach of Lowell.[5]

Kleinendorst was named head coach of USA Hockey National Team Development Program's Under-18 team for the 2010 season, leading the team to a Gold Medal at the 2010 IIHF World U18 Championships.[1] When interviewed about taking the position with USA Hockey, Kleinendorst stated "I could’ve stayed with New Jersey as a scout, but I had already done that. And when Jim Johannson called and asked me to think about this job, it was good timing [...] These are high-school age players and I remember what my high school coaches [at Grand Rapids] meant to me. I know that the Development Program is one of the best programs anywhere and I’m intrigued by working with this age group."[2] Kleinendorst had previously served as Team USA's assistant coach during the 2008 IIHF World Championship.[1]